Whole-genome draft assembly of <i>Populus tremula</i> x <i>P. alba</i> clone INRA 717-1B4

Mäder, Malte; Paslier, Marie‐Christine Le; Bounon, Rémi; Berard, Aurélie; Rampant, Patricia Faivre; Fladung, Matthias; Leplé, Jean‐Charles; Kersten, Birgit

doi:10.1515/sg-2016-0019

Cited by 31 publications

(36 citation statements)

References 22 publications

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“…Genome-wide identification of regions containing targeted genes involved in the nutritional responses can be achieved by conducting comparative ChiP-Seq analysis in poplar ( Liu et al, 2015 ). A recent genomic resource will facilitate this task, the whole genome-assembly of the P. tremula x P. alba clone INRA 717-1B4 that is used as a tree model in transgenic experiments ( Mader et al, 2016 ). New knowledge derived from these studies and/or those derived from the molecular dissection of QTLs will facilitate the identification of genes linking GS1/glutamine biosynthesis and biomass production.…”

Section: Perspectives and Future Developmentsmentioning

confidence: 99%

Nitrogen Metabolism and Biomass Production in Forest Trees

et al. 2018

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Low nitrogen (N) availability is a major limiting factor for tree growth and development. N uptake, assimilation, storage and remobilization are key processes in the economy of this essential nutrient, and its efficient metabolic use largely determines vascular development, tree productivity and biomass production. Recently, advances have been made that improve our knowledge about the molecular regulation of acquisition, assimilation and internal recycling of N in forest trees. In poplar, a model tree widely used for molecular and functional studies, the biosynthesis of glutamine plays a central role in N metabolism, influencing multiple pathways both in primary and secondary metabolism. Moreover, the molecular regulation of glutamine biosynthesis is particularly relevant for accumulation of N reserves during dormancy and in N remobilization that takes place at the onset of the next growing season. The characterization of transgenic poplars overexpressing structural and regulatory genes involved in glutamine biosynthesis has provided insights into how glutamine metabolism may influence the N economy and biomass production in forest trees. Here, a general overview of this research topic is outlined, recent progress are analyzed and challenges for future research are discussed.

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Section: Perspectives and Future Developmentsmentioning

confidence: 99%

Nitrogen Metabolism and Biomass Production in Forest Trees

et al. 2018

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“…Genome sequencing was performed using HiSeq2000 at Macrogen Inc., Korea, and de novo assembly and confirmation were completed using Velvet 1.2.10 (Zerbino and Birney 2008), SOAPGapCloser 1.12 (Zhao et al 2011), BWA 0.7.17 (Li 2013), and SAMtools 1.9 (Li et al 2009). Geneious R11 11.0.5 (Biomatters Ltd, Auckland, New Zealand) was also used for annotation of mitochondrial and chloroplast genomes based on Populus tremula x Populus alba mitochondrial genome (NC_028329; Mader et al 2016) and P. alba chloroplast genome (NC_008235; Okumura et al 2006), respectively.…”

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confidence: 99%

“…Its mitochondrial genome (Genbank accession is MK358443) is 813,261 bp and overall GC content is 44.9%, similar to those of P. tremula x P. alba (783,513bp and 44.7%; Mader et al 2016). It contains 59 genes (32 protein-coding genes, 22 tRNAs, and three rRNAs), which is same to that of P. tremula x P. alba (Mader et al 2016) and less than one protein-coding gene by Arabidopsis thaliana (Unseld et al 1997).…”

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confidence: 99%

The complete chloroplast and mitochondrial genomes of Hyunsasi tree, Populus alba x Populus glandulosa (Salicaceae)

Park¹,

Kim²,

Xi³

et al. 2019

Mitochondrial DNA Part B

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Populus alba x Populus glandulosa is a hybrid species made by Dr. Hyun. It is called as Hyunsasi tree in Korea. It has been used as a good resource for genetic engineering because it is sterile. Here, we presented its complete chloroplast and mitochondrial genomes: chloroplast genome is identical to that of P. alba (156,505 bp and 129 genes covering 84 protein-coding genes, 37 tRNAs, and eight rRNAs) and mitochondrial genome is 813,261 bp long and GC ratio is 44.9%. It contains 59 genes containing 32 protein-coding genes, 22 tRNAs, and three rRNAs. Based on alignment with P. tremula x P. alba mitochondrial genome, 1,752 single nucleotide polymorphisms (SNPs; 0.22%) and 41,506 insertion and deletions (INDELs; 5.10%) are found. Phylogenetic trees based on chloroplast and mitochondrial genomes show different topology in four Populus species, indicating that both genomes may be evolved in different ways after common ancestors of Populus genus.

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“…The high economic importance of poplars has increased scientific interest in them. In different countries, several poplar genomes have been recently sequenced [4][5][6][7][8].…”

Section: Introductionmentioning

confidence: 99%

The Development of Populus alba L. and Populus tremula L. Species Specific Molecular Markers Based on 5S rDNA Non-Transcribed Spacer Polymorphism

Alexandrov

Карлов

2019

Forests

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The Populus L. genus includes tree species that are botanically grouped into several sections. This species successfully hybridizes both in the same section and among other sections. Poplar hybridization widely occurs in nature and in variety breeding. Therefore, the development of poplar species' specific molecular markers is very important. The effective markers for trees of the Aigeiros Duby section have recently been developed using the polymorphism of 5S rDNA non-transcribed spacers (NTSs). In this article, 5S rDNA NTS-based markers were designed for several species of the Leuce Duby section. The alb9 marker amplifies one fragment with the DNA matrix of P. alba and P. × canescens (natural hybrid P. alba × P. tremula). The alb2 marker works the same way, except for the case with Populus bolleana. In this case, the amplification of three fragments was observed. The tremu1 marker amplification was detected with the DNA matrix of P. tremula and P. × canescens. Thus, the developed markers may be applied as a useful tool for P. alba, P. tremula, P. × canescens, and P. bolleana identification in various areas of plant science such as botany, dendrology, genetics of populations, variety breeding, etc.

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Whole-genome draft assembly of Populus tremula x P. alba clone INRA 717-1B4

Cited by 31 publications

References 22 publications

Nitrogen Metabolism and Biomass Production in Forest Trees

Nitrogen Metabolism and Biomass Production in Forest Trees

The complete chloroplast and mitochondrial genomes of Hyunsasi tree, Populus alba x Populus glandulosa (Salicaceae)

The Development of Populus alba L. and Populus tremula L. Species Specific Molecular Markers Based on 5S rDNA Non-Transcribed Spacer Polymorphism

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